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- PDB-5lt1: nucleotide-free kinesin-1 motor domain T92V mutant, P21 crystal form -

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Basic information

Entry
Database: PDB / ID: 5lt1
Titlenucleotide-free kinesin-1 motor domain T92V mutant, P21 crystal form
ComponentsKinesin-like protein
KeywordsMOTOR PROTEIN / Kinesin motor domain / ADP dissociation / nucleotide-free
Function / homology
Function and homology information


regulation of modification of synapse structure, modulating synaptic transmission / plus-end-directed vesicle transport along microtubule / cytoplasm organization / anterograde dendritic transport of neurotransmitter receptor complex / cytolytic granule membrane / anterograde neuronal dense core vesicle transport / mitocytosis / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / vesicle transport along microtubule ...regulation of modification of synapse structure, modulating synaptic transmission / plus-end-directed vesicle transport along microtubule / cytoplasm organization / anterograde dendritic transport of neurotransmitter receptor complex / cytolytic granule membrane / anterograde neuronal dense core vesicle transport / mitocytosis / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / vesicle transport along microtubule / lysosome localization / positive regulation of potassium ion transport / plus-end-directed microtubule motor activity / Kinesins / RHO GTPases activate KTN1 / kinesin complex / microtubule motor activity / centrosome localization / mitochondrion transport along microtubule / COPI-dependent Golgi-to-ER retrograde traffic / ciliary rootlet / microtubule-based movement / stress granule disassembly / natural killer cell mediated cytotoxicity / synaptic vesicle transport / Insulin processing / postsynaptic cytosol / phagocytic vesicle / axon cytoplasm / dendrite cytoplasm / MHC class II antigen presentation / axon guidance / regulation of membrane potential / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / cellular response to type II interferon / centriolar satellite / Signaling by ALK fusions and activated point mutants / microtubule binding / nuclear membrane / vesicle / microtubule / cadherin binding / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Kinesin motor domain / Kinesin / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily ...Kinesin motor domain / Kinesin / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / STRONTIUM ION / Kinesin-1 heavy chain / Kinesin-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å
AuthorsCao, L. / Gigant, B.
Funding support France, 3items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BSV8-0002-01 France
FRISBIANR-10-INSB-05-01 France
ARC France
CitationJournal: Sci Rep / Year: 2017
Title: The structural switch of nucleotide-free kinesin.
Authors: Cao, L. / Cantos-Fernandes, S. / Gigant, B.
History
DepositionSep 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinesin-like protein
B: Kinesin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,16210
Polymers72,5502
Non-polymers6128
Water11,620645
1
A: Kinesin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4894
Polymers36,2751
Non-polymers2143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6736
Polymers36,2751
Non-polymers3985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.903, 69.921, 100.139
Angle α, β, γ (deg.)90.00, 100.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kinesin-like protein / nucleotide-free kinesin-1 T92V mutant


Mass: 36274.773 Da / Num. of mol.: 2 / Mutation: C7S, C65A, T92V, C168A, C174S, C294A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF5B / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q6P164, UniProt: P33176*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Na-Acetate pH 4.5-5.5 23% PEG 4000 0.2 M Ammonium Sulfate 0.1 M SrCl2
PH range: 4.5-5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.949→44 Å / Num. obs: 53434 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 24.18 Å2 / CC1/2: 0.992 / Rrim(I) all: 0.18 / Net I/σ(I): 6.5
Reflection shellRrim(I) all: 1.18

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BG2

1bg2


Resolution: 1.949→43.353 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.41
RfactorNum. reflection% reflectionSelection details
Rfree0.2359 2007 3.76 %RANDOM
Rwork0.1945 ---
obs0.196 53340 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.949→43.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4813 0 32 645 5490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084912
X-RAY DIFFRACTIONf_angle_d1.1816630
X-RAY DIFFRACTIONf_dihedral_angle_d13.0461806
X-RAY DIFFRACTIONf_chiral_restr0.049752
X-RAY DIFFRACTIONf_plane_restr0.005860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9486-1.99730.30911570.29323596X-RAY DIFFRACTION97
1.9973-2.05130.30971320.25643629X-RAY DIFFRACTION100
2.0513-2.11170.26051320.23133652X-RAY DIFFRACTION100
2.1117-2.17980.26741500.23023669X-RAY DIFFRACTION100
2.1798-2.25770.26531480.21543653X-RAY DIFFRACTION100
2.2577-2.34810.26881420.21483663X-RAY DIFFRACTION100
2.3481-2.4550.26671380.20873669X-RAY DIFFRACTION100
2.455-2.58440.23251450.19923651X-RAY DIFFRACTION100
2.5844-2.74630.24491500.19583649X-RAY DIFFRACTION100
2.7463-2.95830.24771340.19713687X-RAY DIFFRACTION100
2.9583-3.25590.22721440.18083663X-RAY DIFFRACTION100
3.2559-3.72680.18791410.16683698X-RAY DIFFRACTION100
3.7268-4.69450.19311450.15333699X-RAY DIFFRACTION100
4.6945-43.36370.24141490.1963755X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3321-0.2195-0.38981.42340.1221.1456-0.03620.0742-0.0243-0.0008-0.00280.09540.0576-0.08550.03540.1069-0.01920.01560.1245-0.00150.1561-38.5998-8.6529-1.0635
20.65250.40710.14131.43260.35990.8664-0.0572-0.00230.03730.02830.030.052-0.0226-0.06310.02140.08450.01740.00460.12790.01170.1272-29.4794-8.874-48.0665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 7 through 324)
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 325)

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